Base Info

An object of class Seurat 35687 features across 11553 samples within 2 assays Active assay: SCT (15863 features) 1 other assay present: RNA 3 dimensional reductions calculated: pca, umap, tsne

The Seurat object was generated with Seurat 3.1.4.

Table of Data

Class Data

Annotated Cell Types

Calculated Clusters

Interactive Plot

Downsampled to 1000 cells.

Environment

## R version 3.6.3 (2020-02-29)
## Platform: x86_64-apple-darwin18.7.0 (64-bit)
## Running under: macOS Mojave 10.14.6
## 
## Matrix products: default
## BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
## LAPACK: /usr/local/Cellar/openblas/0.3.9/lib/libopenblasp-r0.3.9.dylib
## 
## locale:
## [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] Seurat_3.1.0   plotly_4.9.2.1 knitr_1.28     dplyr_0.8.5    ggplot2_3.3.0  rmarkdown_2.1 
## 
## loaded via a namespace (and not attached):
##   [1] tsne_0.1-3          nlme_3.1-147        RcppAnnoy_0.0.16    RColorBrewer_1.1-2  httr_1.4.1          numDeriv_2016.8-1.1
##   [7] sctransform_0.2.1   tools_3.6.3         R6_2.4.1            irlba_2.3.3         KernSmooth_2.23-17  uwot_0.1.8         
##  [13] BiocGenerics_0.30.0 lazyeval_0.2.2      colorspace_1.4-1    sn_1.6-1            npsurv_0.4-0.1      withr_2.2.0        
##  [19] gridExtra_2.3       tidyselect_1.0.0    mnormt_1.5-7        compiler_3.6.3      Biobase_2.44.0      TFisher_0.2.0      
##  [25] sandwich_2.5-1      labeling_0.3        scales_1.1.0        lmtest_0.9-37       mvtnorm_1.1-0       pbapply_1.4-2      
##  [31] ggridges_0.5.2      stringr_1.4.0       digest_0.6.25       R.utils_2.9.2       pkgconfig_2.0.3     htmltools_0.4.0    
##  [37] bibtex_0.4.2.2      plotrix_3.7-8       htmlwidgets_1.5.1   rlang_0.4.6         farver_2.0.3        zoo_1.8-8          
##  [43] jsonlite_1.6.1      crosstalk_1.1.0.1   ica_1.0-2           R.oo_1.23.0         magrittr_1.5        Matrix_1.2-18      
##  [49] Rcpp_1.0.4.6        munsell_0.5.0       ape_5.3             reticulate_1.15     lifecycle_0.2.0     R.methodsS3_1.8.0  
##  [55] multcomp_1.4-13     stringi_1.4.6       yaml_2.2.1          gbRd_0.4-11         MASS_7.3-51.6       Rtsne_0.15         
##  [61] plyr_1.8.6          grid_3.6.3          parallel_3.6.3      listenv_0.8.0       ggrepel_0.8.2       crayon_1.3.4       
##  [67] lattice_0.20-41     cowplot_1.0.0       splines_3.6.3       multtest_2.40.0     SDMTools_1.1-221.2  pillar_1.4.4       
##  [73] igraph_1.2.5        reshape2_1.4.4      future.apply_1.5.0  codetools_0.2-16    stats4_3.6.3        leiden_0.3.3       
##  [79] mutoss_0.1-12       glue_1.4.0          evaluate_0.14       lsei_1.2-0.1        metap_1.3           data.table_1.12.8  
##  [85] png_0.1-7           vctrs_0.2.4         Rdpack_0.11-1       gtable_0.3.0        RANN_2.6.1          purrr_0.3.4        
##  [91] tidyr_1.0.3         future_1.17.0       assertthat_0.2.1    xfun_0.13           rsvd_1.0.3          survival_3.1-12    
##  [97] viridisLite_0.3.0   tibble_3.0.1        cluster_2.1.0       globals_0.12.5      TH.data_1.0-10      fitdistrplus_1.0-14
## [103] ellipsis_0.3.0      ROCR_1.0-11